This program is designed to reformat all the tables of the database into a set of XML files which will be used by the analysis programs.
Option | Usage | Type | Explanation
|
---|---|---|---|
-e,--exp | required | string | Experiment file
|
-o,--output | required | string | Output XML directory
|
-m,--mapdb | required | string | The GLMdb directory
|
-q,--qtldb | optional | string | The QTLdb directory
|
-t,--tofile | optional | string | Trait Ontology file
|
-d,--mrkdico | optional | string | Marker dictionary file
|
--mrkup | optional | string | A file with the marker name to update
|
--mrkrm | optional | string | A file with the marker to remove
|
--chrm | optional | string | A file with the chromosome to remove
|
For example, suppose we have created a database which consists in the files exp.txt (experiment table), onto.txt (trait ontology), dico.txt (marker dictionary), and the directories glmdb/ and qtldb/ which contain the marker map and the QTL map tables relative to the mapping experiments specified in exp.txt. We assume that all the files and directories are included into the same directory, the database directory. Then we can create the XML repository, xmldb/, by invoking the command (in the database directory)
>java org.metaqtl.main.MetaDB \ -e exp.txt -t onto.txt -d dico.txt -m glmdb -q qtldb -o xmldb |
For the option --mrkup
, the input file format must be a table with 4 columns seperated by a tabulation as follows:
Exp1 Chrom1 mrk3 mrk3a Exp1 Chrom2 mrk4 mrk4b Exp2 Chrom1 mrk1 mrk1c ...
where the first column gives the name of the mapping experiment (must be the same than in the experiment table), the second the name of the chromosome, the third one the current name of the marker to update and the last one the new name of the marker.
For the option --mrkrm
, the input file is the same than the previous one except that it contains only the first three columns.
Finally, for the option --chrm
, the input file is the same than the previous one except that it contains only the first two columns.
Note that these three last options have no effect on the raw data file: the rules they define are only applied to the ouput XML data base.